Evidence for the relatively close relationship of archaea to eukaryotes includes

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Archaea and eukaryotes both have several kinds of relatively complex RNA polymerases, while bacteria have a single, less complex RNA polymerase. This is evidence of a closer evolutionary relationship between archaea and eukaryotes. Peptidoglycan is found in the cell walls of bacteria, but not in archaea or eukaryotes, and the absence of introns is a characteristic of bacteria, not eukaryotes or archaea. While both archaea and eukaryotes have circular DNA, eukaryotic DNA is wrapped around histone proteins, while archaeal DNA is not.

Evidence for the Relatively Close Relationship of Archaea to Eukaryotes